Cited by 2,759Protein Structure and DynamicsEnzyme Structure and FunctionRNA and protein synthesis mechanisms

The DOI matches its Crossref record; 23 of the 23 references it cites were found in a registry or an index.

The FoldX web server: an online force field

Open access

Schymkowitz, J., Borg, J., Stricher, F., Nys, R., Rousseau, F., Serrano, L.·2005·Nucleic Acids Research

Open this paper in CoChat — free account Open PDF

Abstract

FoldX is an empirical force field that was developed for the rapid evaluation of the effect of mutations on the stability, folding and dynamics of proteins and nucleic acids. The core functionality of FoldX, namely the calculation of the free energy of a macromolecule based on its high-resolution 3D structure, is now publicly available through a web server at http://foldx.embl.de/. The current release allows the calculation of the stability of a protein, calculation of the positions of the protons and the prediction of water bridges, prediction of metal binding sites and the analysis of the free energy of complex formation. Alanine scanning, the systematic truncation of side chains to alanine, is also included. In addition, some reporting functions have been added, and it is now possible to print both the atomic interaction networks that constitute the protein, print the structural and energetic details of the interactions per atom or per residue, as well as generate a general quality report of the pdb structure. This core functionality will be further extended as more FoldX applications are developed.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1093/nar/gki387

Cites

23 of 23 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

SWISS‐MODEL and the Swiss‐Pdb Viewer: An environment for comparative protein modeling
Guex, N., & Peitsch, M. C. (1997) · Electrophoresis · doi:10.1002/elps.1150181505 · Cited by 11,297 · cited 1×
“Although the pdb-reader in FoldX is continually extended to handle more exceptions, standardizing the format of anomalous ﬁles most often solves the problem—this can easily be achieved by opening and saving the ﬁle using Swiss PDB viewer (14) or WHATIF (15).”
Method
The interpretation of protein structures: Estimation of static accessibility
Lee, B., & Richards, F. M. (1971) · Journal of Molecular Biology · doi:10.1016/0022-2836(71)90324-x · Cited by 5,884 · cited 1×
“The occupancy of an atom i, Occ(i), is calculated using an envelope function (21) with a distance cut-off of 6 s (9).”
Method
WHAT IF: A molecular modeling and drug design program
Vriend, G. (1990) · Journal of Molecular Graphics · doi:10.1016/0263-7855(90)80070-v · Cited by 3,476 · cited 1×
“Although the pdb-reader in FoldX is continually extended to handle more exceptions, standardizing the format of anomalous ﬁles most often solves the problem—this can easily be achieved by opening and saving the ﬁle using Swiss PDB viewer (14) or WHATIF (15).”
Method
Predicting Changes in the Stability of Proteins and Protein Complexes: A Study of More Than 1000 Mutations
Guerois, R., Nielsen, J. E., & Serrano, L. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00442-4 · Cited by 1,728 · cited 3×
“In addition, those water molecules that have a persistent interaction with groups of the protein, i.e. make more than two hydrogen bonds with the protein, are calculated explicitly in the D G wb term (8,9).”
BackgroundMethodInfluentialSelf-citation
Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins
Fernández‐Escamilla, A. M., Rousseau, F., Schymkowitz, J. W. H., & Serrano, L. G. (2004) · Nature Biotechnology · doi:10.1038/nbt1012 · Cited by 1,667 · cited 1×
“In this fashion, TANGO predicts correctly both the disease causing and protective mutations in a wide range of proteins including Alzheimers’ A b peptide, lysozyme and transthyretin (12).”
BackgroundSelf-citation
Biased Probability Monte Carlo Conformational Searches and Electrostatic Calculations for Peptides and Proteins
Abagyan, R. A., & Totrov, M. M. (1994) · Journal of Molecular Biology · doi:10.1006/jmbi.1994.1052 · Cited by 982 · cited 8×
“The statistical mechanics algorithm TANGO, publicly available at http:// TANGO.embl.de/, provides such a predictive model.”
MethodInfluential
Molecular basis for amyloid fibril formation and stability
Makin, O. S., Atkins, E. D. T., Sikorski, P., Johansson, J., & Serpell, L. C. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0406847102 · Cited by 649 · cited 1×
“For protein aggregation no such detail is available, although recently the ﬁrst ever crystal structure of an amyloid ﬁbre was released (23).”
Background
Effective energy functions for protein structure prediction
Lazaridis, T. (2000) · Current Opinion in Structural Biology · doi:10.1016/s0959-440x(00)00063-4 · Cited by 445 · cited 1×
“These are designated by Lazaridis and Karplus (1) as statistical (SEEF) and physical (PEEF) effective energy functions, respectively.”
Background
Protein-misfolding diseases: Getting out of shape
Dobson, C. M. (2002) · Nature · doi:10.1038/418729a · Cited by 341 · cited 1×
“The crystal structure conﬁrms the widespread observation in the ﬁeld that protein aggregates are generally rich in cross-beta structure (24), which allows a low-resolution structural approach to predict protein aggregation.”
Background
Rational design of faster associating and tighter binding protein complexes.
Schreiber, G., Selzer, T., & Albeck, S. (2000) · Nature Structural Biology · doi:10.1038/76744 · Cited by 299 · cited 1×
“(10), which was shown to give a good estimation of the association rate ( k on ) of complex formation.”
Background

Flagged first, then by citations

Show all 23 references

Sorted by citations

Items 501–600 of 1,005

Quantifying information transfer by protein domains: Analysis of the Fyn SH2 domain structure
Lenaerts, T., Ferkinghoff‐Borg, J., Stricher, F., Serrano, L. G., Schymkowitz, J. W. H., & Rousseau, F. (2008) · BMC Structural Biology · doi:10.1186/1472-6807-8-43 · Cited by 40
Self-citation
Asymmetrical dose responses shape the evolutionary trade-off between antifungal resistance and nutrient use
Després, P. C., Cisneros, A. F., Alexander, E. M. M., Sonigara, R., Gagné-Thivierge, C., Dubé, A. K., & Landry, C. R. (2022) · Nature Ecology & Evolution · doi:10.1038/s41559-022-01846-4 · Cited by 32
Evidence of Positive Selection in Mitochondrial Complexes I and V of the African Elephant
Finch, T., Zhao, N., Korkin, D., Frederick, K., & Eggert, L. S. (2014) · PLoS ONE · doi:10.1371/journal.pone.0092587 · Cited by 39
The Conserved His-144 in the PsbP Protein Is Important for the Interaction between the PsbP N-terminus and the Cyt b559 Subunit of Photosystem II
Ido, K., Kakiuchi, S., Uno, C., et al. (2012) · Journal of Biological Chemistry · doi:10.1074/jbc.m112.385286 · Cited by 39
Energetic determinants of protein binding specificity: Insights into protein interaction networks
Carbonell, P., Nussinov, R., & del Sol, A. (2009) · PROTEOMICS · doi:10.1002/pmic.200800425 · Cited by 39
Mechanisms of Intramolecular Communication in a Hyperthermophilic Acylaminoacyl Peptidase: A Molecular Dynamics Investigation
Papaleo, E., Renzetti, G., & Tiberti, M. (2012) · PLoS ONE · doi:10.1371/journal.pone.0035686 · Cited by 39
Structure-based prediction of the effects of a missense variant on protein stability
Yang, Y., Chen, B., Tan, G., Vihinen, M., & Shen, B. (2012) · Amino Acids · doi:10.1007/s00726-012-1407-7 · Cited by 39
Roles of residues in the interface of transient protein-protein complexes before complexation
Swapna, L. S., Bhaskara, R. M., Sharma, J. N., & Srinivasan, N. (2012) · Scientific Reports · doi:10.1038/srep00334 · Cited by 38
Molecular modeling indicates distinct classes of missense variants with mild and severe XLRS phenotypes
Sergeev, Y. V., Vitale, S., Sieving, P. A., Vincent, A., Robson, A. G., Moore, A. T., Webster, A. R., & Holder, G. E. (2013) · Human Molecular Genetics · doi:10.1093/hmg/ddt329 · Cited by 41
Target Based Drug Design - A Reality in Virtual Sphere
Verma, S. K., & Prabhakar, Y. S. (2015) · Current Medicinal Chemistry · doi:10.2174/0929867322666150209151209 · Cited by 43
Germline-Derived Gain-of-Function Variants of Gsα-Coding GNAS Gene Identified in Nephrogenic Syndrome of Inappropriate Antidiuresis
Miyado, M., Fukami, M., Takada, S., Terao, M., Nakabayashi, K., Hata, K., Matsubara, Y., Tanaka, Y., Sasaki, G., Nagasaki, K., et al. (2019) · Journal of the American Society of Nephrology · doi:10.1681/asn.2018121268 · Cited by 38
Changes in gene expression predictably shift and switch genetic interactions
Li, X., Lalić, J., Baeza-Centurión, P., Dhar, R., & Lehner, B. (2019) · Nature Communications · doi:10.1038/s41467-019-11735-3 · Cited by 38
Damaging de novo missense variants inEEF1A2lead to a developmental and degenerative epileptic‐dyskinetic encephalopathy
Carvill, G. L., Helbig, K. L., Myers, C. T., Scala, M., Huether, R., Lewis, S. A., Kruer, T. N., Guida, B. S., Bakhtiari, S., Sebe, J. Y., et al. (2020) · Human Mutation · doi:10.1002/humu.24015 · Cited by 39
An in vivo platform to select and evolve aggregation-resistant proteins
Ebo, J. S., Saunders, J. C., Devine, P. W. A., Gordon, A., Warwick, A. S., Schiffrin, B., Chin, S. E., England, E., Button, J. D., Lloyd, C., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-15667-1 · Cited by 34
CompassR Yields Highly Organic‐Solvent‐Tolerant Enzymes through Recombination of Compatible Substitutions
Cui, H., Jaeger, K., Davari, M. D., et al. (2020) · Chemistry - A European Journal · doi:10.1002/chem.202004471 · Cited by 39
Protein quality control and regulated proteolysis in the genome‐reduced organism Mycoplasma pneumoniae
Burgos, R., Weber, M., Martinez, S., Lluch‐Senar, M., & Serrano, L. (2020) · Molecular Systems Biology · doi:10.15252/msb.20209530 · Cited by 39
Self-citation
CompassR-guided recombination unlocks design principles to stabilize lipases in ILs with minimal experimental efforts
Cui, H., Pramanik, S., Jaeger, K., et al. (2021) · Green Chemistry · doi:10.1039/d1gc00763g · Cited by 39
Three Simple Properties Explain Protein Stability Change upon Mutation
Caldararu, O. F., Blundell, T. L., & Kepp, K. P. (2021) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.1c00201 · Cited by 40
Global Genomic Analysis of SARS-CoV-2 RNA Dependent RNA Polymerase Evolution and Antiviral Drug Resistance
Mari, A., Roloff, T. C., Stange, M., Søgaard, K. K., Asllanaj, E., Tauriello, G., Alexander, L. T., Schweitzer, M., Leuzinger, K., Gensch, A., et al. (2021) · Microorganisms · doi:10.3390/microorganisms9051094 · Cited by 37
Implications of disease-related mutations at protein–protein interfaces
Xiong, D., Lee, D., Li, L., Zhao, Q., & Yu, H. (2021) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2021.11.012 · Cited by 40
Approaches to expand the conventional toolbox for discovery and selection of antibodies with drug-like physicochemical properties
Svilenov, H. L., Arosio, P., Menzen, T., Tessier, P. M., & Sormanni, P. (2023) · mAbs · doi:10.1080/19420862.2022.2164459 · Cited by 40
Impact of Rett Syndrome Mutations on MeCP2 MBD Stability
Kucukkal, T. G., Yang, Y., Uvarov, O., Cao, W., & Alexov, E. (2015) · Biochemistry · doi:10.1021/acs.biochem.5b00790 · Cited by 39
Structural Modeling of GR Interactions with the SWI/SNF Chromatin Remodeling Complex and C/EBP
Muratcioglu, S., Presman, D. M., Pooley, J. R., Grøntved, L., Hager, G. L., Nussinov, R., Keskin, O., & Gursoy, A. (2015) · Biophysical Journal · doi:10.1016/j.bpj.2015.06.044 · Cited by 39
TRIM21 is a druggable target for the treatment of metastatic colorectal cancer through ubiquitination and activation of MST2
Liu, Y.-X., Wan, S., Yang, X., Wang, Y., Gan, W.-J., Ye, W.-L., He, X., Chen, J.-J., Yang, Y., Yang, X., et al. (2023) · Cell chemical biology · doi:10.1016/j.chembiol.2023.05.009 · Cited by 42
Improving the prediction of protein stability changes upon mutations by geometric learning and a pre-training strategy
Xu, Y., Liu, D., & Gong, H. (2024) · Nature Computational Science · doi:10.1038/s43588-024-00716-2 · Cited by 41
Predicting absolute protein folding stability using generative models
Cagiada, M., Ovchinnikov, S., & Lindorff‐Larsen, K. (2024) · Protein Science · doi:10.1002/pro.5233 · Cited by 38
An Evolutionary Analysis of Antigen Processing and Presentation across Different Timescales Reveals Pervasive Selection
Forni, D., Cagliani, R., Tresoldi, C., Pozzoli, U., GIOIA, L. D., Filippi, G., Riva, S., Menozzi, G., Colleoni, M., Biasin, M., et al. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004189 · Cited by 37
SiteComp: a server for ligand binding site analysis in protein structures
Lin, Y., Yoo, S., & Sánchez, R. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts095 · Cited by 38
Prediction of Protein Hotspots from Whole Protein Sequences by a Random Projection Ensemble System
Jiang, J., Wang, N., Chen, P., Zheng, C.-H., & Wang, B. (2017) · International Journal of Molecular Sciences · doi:10.3390/ijms18071543 · Cited by 38
A recombinant Fasciola gigantica 14-3-3 epsilon protein (rFg14-3-3e) modulates various functions of goat peripheral blood mononuclear cells
Tian, A.-L., Lu, M., Calderón-Mantilla, G., Petsalaki, E., Dottorini, T., Tian, X., Wang, Y., Huang, S., Hou, J.-L., Li, X., et al. (2018) · Parasites & Vectors · doi:10.1186/s13071-018-2745-4 · Cited by 36
The Tumor Suppressor ING5 Is a Dimeric, Bivalent Recognition Molecule of the Histone H3K4me3 Mark
Ormaza, G., Buitrago, J. A. R., de Opakua, A. I., Merino, N., Villate, M., Gorroño‐Etxebarria, I., Rábano, M., Palmero, I., Vilaseca, M., Kypta, R. M., et al. (2019) · Journal of Molecular Biology · doi:10.1016/j.jmb.2019.04.018 · Cited by 39
The Staphylococcus aureus Two-Component System AgrAC Displays Four Distinct Genomic Arrangements That Delineate Genomic Virulence Factor Signatures
Choudhary, K. S., Mih, N., Monk, J. M., Kavvas, E. S., Yurkovich, J. T., Sakoulas, G., & Palsson, B. Ø. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.01082 · Cited by 38
Predicting and designing therapeutics against the Nipah virus
Sen, N., Kanitkar, T. R., Roy, A., Soni, N., Amritkar, K., Supekar, S., Nair, S. A., Singh, G., & Madhusudhan, M. S. (2019) · PLoS neglected tropical diseases · doi:10.1371/journal.pntd.0007419 · Cited by 38
Autonomous aggregation suppression by acidic residues explains why chaperones favour basic residues
Houben, B., Michiels, E., Ramakers, M., Konstantoulea, K., Louros, N. N., Verniers, J., van der Kant, R., Vleeschouwer, M. D., Chicória, N., Vanpoucke, T., et al. (2020) · The EMBO Journal · doi:10.15252/embj.2019102864 · Cited by 37
Self-citation
Differential Effects of IGF-1R Small Molecule Tyrosine Kinase Inhibitors BMS-754807 and OSI-906 on Human Cancer Cell Lines
Fuentes-Baile, M., Ventero, M. P., Encinar, J. A., García-Morales, P., Poveda-Deltell, M., Pérez-Valenciano, E., Barberá, V. M., Gallego-Plazas, J., Rodríguez-Lescure, Á., Martín‐Nieto, J., et al. (2020) · Cancers · doi:10.3390/cancers12123717 · Cited by 38
Predicted structural mimicry of spike receptor-binding motifs from highly pathogenic human coronaviruses
Beaudoin, C. A., Jamasb, A. R., Alsulami, A. F., Copoiu, L., van Tonder, A. J., Hala, S. M., Bannerman, B. P., Thomas, S. E., Vedithi, S. C., Torres, P. H. M., et al. (2021) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2021.06.041 · Cited by 36
Communication Routes in ARID Domains between Distal Residues in Helix 5 and the DNA-Binding Loops
Invernizzi, G., Tiberti, M., Lambrughi, M., Lindorff‐Larsen, K., & Papaleo, E. (2014) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003744 · Cited by 36
On the effect of protein conformation diversity in discriminating among neutral and disease related single amino acid substitutions
Juritz, E., Fornasari, M. S., Martelli, P. L., Fariselli, P., Casadio, R., & Parisi, G. D. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-s4-s5 · Cited by 38
Application of Assisted Design of Antibody and Protein Therapeutics (ADAPT) improves efficacy of a Clostridium difficile toxin A single-domain antibody
Sulea, T. I., Hussack, G., Ryan, S., Tanha, J., & Purisima, E. O. (2018) · Scientific Reports · doi:10.1038/s41598-018-20599-4 · Cited by 38
PRIM1 deficiency causes a distinctive primordial dwarfism syndromePreprint
Parry, D. A., Tamayo-Orrego, L., Carroll, P., Marsh, J., Greene, P., Murina, O., Uggenti, C., Leitch, A., Partnership, S., Káposzta, R., et al. (2020) · Genes & Development · doi:10.1101/gad.340190.120 · Cited by 29
ChaperISM: improved chaperone binding prediction using position-independent scoring matrices
Gutierres, M. B. B., Bonorino, C. B. C., & Rigo, M. M. (2020) · Bioinformatics · doi:10.1093/bioinformatics/btz670 · Cited by 29
VIPdb, a genetic variant impact predictor database
Hu, Z., Yu, C., Furutsuki, M., Andreoletti, G., Ly, M., Hoskins, R., Adhikari, A. N., & Brenner, S. E. (2019) · Human Mutation · doi:10.1002/humu.23858 · Cited by 37
SLITRK2 variants associated with neurodevelopmental disorders impair excitatory synaptic function and cognition in mice
Chehadeh, S. E., Han, K. A., Kim, D., Jang, G., Bakhtiari, S., Lim, D., Kim, H. Y., Kim, J., Kim, H., Wynn, J., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-31566-z · Cited by 37
Network of epistatic interactions in an enzyme active site revealed by large-scale deep mutational scanning
Judge, A., Sankaran, B., Hu, L., Palaniappan, M., Birgy, A., Prasad, B. V. V., & Palzkill, T. G. (2024) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2313513121 · Cited by 37
AI for organic and polymer synthesis
Hong, X., Yang, Q., Liao, K., Pei, J., Chen, M., Mo, F., Lu, H., Zhang, W.-B., Zhou, H., Chen, J., et al. (2024) · Science China Chemistry · doi:10.1007/s11426-024-2072-4 · Cited by 41
The expanding spectrum of PRPS1-associated phenotypes: three novel mutations segregating with X-linked hearing loss and mild peripheral neuropathy
Robusto, M., Fang, M., Asselta, R., Castorina, P., Previtali, S. C., Caccia, S., Benzoni, E., CRISTOFARO, R. D., Yu, C., Cesarani, A., et al. (2014) · European Journal of Human Genetics · doi:10.1038/ejhg.2014.168 · Cited by 37
Computational and Experimental Approaches to Reveal the Effects of Single Nucleotide Polymorphisms with Respect to Disease Diagnostics
Kucukkal, T. G., Yang, Y., Chapman, S. C., Cao, W., & Alexov, E. (2014) · International Journal of Molecular Sciences · doi:10.3390/ijms15069670 · Cited by 40
The role of salt bridges on the temperature adaptation of aqualysin I, a thermostable subtilisin-like proteinase
Jónsdóttir, L. B., Ellertsson, B. Ö., Invernizzi, G., et al. (2014) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2014.08.011 · Cited by 37
Towards Increasing the Clinical Relevance of In Silico Methods to Predict Pathogenic Missense Variants
Masica, D. L., & Karchin, R. (2016) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004725 · Cited by 36
Computational Tools for Designing Smart Libraries
Šebestová, E., Bendl, J. M., Brezovský, J., & Damborský, J. (2014) · Methods in molecular biology · doi:10.1007/978-1-4939-1053-3_20 · Cited by 37
The FtsLB subcomplex of the bacterial divisome is a tetramer with an uninterrupted FtsL helix linking the transmembrane and periplasmic regions
Condon, S. G. F., Mahbuba, D., Armstrong, C. R., Vázquez, G. D., Craven, S. J., LaPointe, L. M., Khadria, A. S., Chadda, R., Crooks, J. A., Rangarajan, N., et al. (2017) · Journal of Biological Chemistry · doi:10.1074/jbc.ra117.000426 · Cited by 35
Adaptive Mutations in RNA Polymerase and the Transcriptional Terminator Rho Have Similar Effects on Escherichia coli Gene Expression
González‐González, A., Hug, S. M., Rodríguez‐Verdugo, A., Patel, J. S., & Gaut, B. S. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx216 · Cited by 39
The conformational and mutational landscape of the ubiquitin-like marker for autophagosome formation in cancer
Fas, B. A., Maiani, E., Sora, V., Kumar, M., Mashkoor, M., Lambrughi, M., Tiberti, M., & Papaleo, E. (2020) · Autophagy · doi:10.1080/15548627.2020.1847443 · Cited by 35
Improving the thermostability of methyl parathion hydrolase from Ochrobactrum sp. M231 using a computationally aided method
Tian, J., Wang, P., Huang, L., Chu, X., Wu, N., & Fan, Y. (2012) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-012-4411-7 · Cited by 37
Improving thermostability of papain through structure-based protein engineering
Choudhury, D., Biswas, S., Roy, S., & Dattagupta, J. Κ. (2010) · Protein Engineering Design and Selection · doi:10.1093/protein/gzq016 · Cited by 37
Brain catecholamine depletion and motor impairment in aThknock-in mouse with type B tyrosine hydroxylase deficiency
Korner, G., Noaín, D., Ying, M., Hole, M., Flydal, M. I., Scherer, T., Allegri, G., Rassi, A., Fingerhut, R., Becú‐Villalobos, D., et al. (2015) · Brain · doi:10.1093/brain/awv224 · Cited by 37
Epistasis between promoter activity and coding mutations shapes gene evolvability
Cisneros, A. F., Gagnon-Arsenault, I., Dubé, A. K., Després, P. C., Kumar, P., Lafontaine, K., Pelletier, J. N., & Landry, C. R. (2023) · Science Advances · doi:10.1126/sciadv.add9109 · Cited by 33
FOXI3 pathogenic variants cause one form of craniofacial microsomia
Mao, K., Borel, C., Ansar, M., Jolly, A., Makrythanasis, P., Froehlich, C., Iwaszkiewicz, J., Wang, B., Xu, X., Li, Q., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-37703-6 · Cited by 35
Engineering and Expression Strategies for Optimization of L-Asparaginase Development and Production
Shishparenok, A. N., Gladilina, Y. A., & Zhdanov, D. D. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms242015220 · Cited by 40
The Region Adjacent to the C-end of the Inner Gate in Transient Receptor Potential Melastatin 8 (TRPM8) Channels Plays a Central Role in Allosteric Channel Activation
Taberner, F. J., López-Córdoba, A., Fernandez-Ballester, G. J., Korchev, Y. E., & Ferrer-Montiel, A. V. (2014) · Journal of Biological Chemistry · doi:10.1074/jbc.m114.577478 · Cited by 36
Evolutionary Conservation of a GPCR-Independent Mechanism of Trimeric G Protein Activation
Coleman, B., Marivin, A., Parag‐Sharma, K., DiGiacomo, V., Kim, S., Pepper, J. S., Casler, J. C., Nguyen, L. T., Koelle, M. R., & Garcia‐Marcos, M. (2015) · Molecular Biology and Evolution · doi:10.1093/molbev/msv336 · Cited by 36
Biasing the native α-synuclein conformational ensemble towards compact states abolishes aggregation and neurotoxicity
Čarija, A., Pinheiro, F., Pujols, J., Brás, I. C., Lázaro, D. F., Santambrogio, C., Grandori, R., Outeiro, T. F., Navarro, S., & Ventura, S. (2019) · Redox Biology · doi:10.1016/j.redox.2019.101135 · Cited by 39
A non‐synonymous SNP in exon 3 of the KIT gene is responsible for the classic grey phenotype in alpacas (Vicugna pacos)
Jones, M., Sergeant, C., Richardson, M. F., et al. (2019) · Animal Genetics · doi:10.1111/age.12814 · Cited by 36
VRK1 functional insufficiency due to alterations in protein stability or kinase activity of human VRK1 pathogenic variants implicated in neuromotor syndromes
Martín‐Doncel, E., Rojas, A. M., Cantarero, L., & Lazo, P. A. (2019) · Scientific Reports · doi:10.1038/s41598-019-49821-7 · Cited by 36
Convolution Neural Network-Based Prediction of Protein Thermostability
Fang, X., Huang, J., Zhang, R., Wang, F., Zhang, Q., Li, G., Yan, J., Zhang, H., Yan, Y., & Xu, L. (2019) · Journal of Chemical Information and Modeling · doi:10.1021/acs.jcim.9b00220 · Cited by 36
Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2
Nguyen, K., Chakraborty, S., Mansbach, R. A., Korber, B., & Gnanakaran, S. (2021) · Viruses · doi:10.3390/v13050927 · Cited by 38
Deimmunization of flagellin for repeated administration as a vaccine adjuvant
Khim, K., Bang, Y. J., Puth, S., Choi, Y., Lee, Y. S., Jeong, K., Lee, S. E., & Rhee, J. H. (2021) · npj Vaccines · doi:10.1038/s41541-021-00379-4 · Cited by 37
Assessing the clinical utility of protein structural analysis in genomic variant classification: experiences from a diagnostic laboratory
Caswell, R. C., Gunning, A. C., Owens, M., Ellard, S., & Wright, C. F. (2022) · Genome Medicine · doi:10.1186/s13073-022-01082-2 · Cited by 42
Novel high‐affinity binders of human interferon gamma derived from albumin‐binding domain of protein G
Ahmad, J. N., Li, J., Biedermannová, L., et al. (2011) · Proteins Structure Function and Bioinformatics · doi:10.1002/prot.23234 · Cited by 36
Protein structure and phenotypic analysis of pathogenic and population missense variants in STXBP1
Suri, M., Evers, J. M. G., Laskowski, R. A., O’Brien, S., Baker, K., Clayton‐Smith, J., Dabir, T. A., Josifova, D. J., Joss, S. K., Kerr, B. A., et al. (2017) · Molecular Genetics & Genomic Medicine · doi:10.1002/mgg3.304 · Cited by 36
A Genome-wide Ras-Effector Interaction Network
Kiel, C., Foglierini, M., Kuemmerer, N., Beltrão, P., & Serrano, L. G. (2007) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.05.015 · Cited by 36
Self-citation
Natural Selection on the Phase-Separation Properties of FUS during 160 My of Mammalian Evolution
Dasmeh, P., & Wagner, A. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa258 · Cited by 36
Rational-Design Engineering to Improve Enzyme Thermostability
Pongsupasa, V., Anuwan, P., Maenpuen, S., & Wongnate, T. (2021) · Methods in molecular biology · doi:10.1007/978-1-0716-1826-4_9 · Cited by 37
Recent advances in structure‐based enzyme engineering for functional reconstruction
Xu, S., Zhou, L., Xu, Y., Hong, H., Dai, C., Wang, Y., & Zheng, Y. (2023) · Biotechnology and Bioengineering · doi:10.1002/bit.28540 · Cited by 39
Protein stability prediction by fine-tuning a protein language model on a mega-scale dataset
Chu, S. K. S., Narang, K., & Siegel, J. B. (2024) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1012248 · Cited by 39
Protein Engineering for Industrial Biocatalysis: Principles, Approaches, and Lessons from Engineered PETases
Grigorakis, K., Ferousi, C., & Topakas, E. (2025) · Catalysts · doi:10.3390/catal15020147 · Cited by 39
Mutations in the histamineN-methyltransferase gene,HNMT, are associated with nonsyndromic autosomal recessive intellectual disability
Heidari, A., Tongsook, C., Najafipour, R., Musante, L., Vasli, N., Garshasbi, M., Hu, H., Mittal, K., McNaughton, A. J. M., Sritharan, K., et al. (2015) · Human Molecular Genetics · doi:10.1093/hmg/ddv286 · Cited by 34
Directed arginine deiminase evolution for efficient inhibition of arginine-auxotrophic melanomas
Cheng, F., Zhu, L., Lue, H., et al. (2014) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-014-5985-z · Cited by 35
The Mutational Landscape of the Oncogenic MZF1 SCAN Domain in Cancer
Nygaard, M. M., Terkelsen, T., Olsen, A. V., Sora, V., Viloria, J. S., Rizza, F., Bergstrand-Poulsen, S., Marco, M. D., Vistesen, M. V., Tiberti, M., et al. (2016) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2016.00078 · Cited by 31
Mistranslation can enhance fitness through purging of deleterious mutations
Bratulić, S., Toll‐Riera, M., & Wagner, A. (2017) · Nature Communications · doi:10.1038/ncomms15410 · Cited by 33
Whole genome SNP-associated signatures of local adaptation in honeybees of the Iberian Peninsula
Henriques, D., Wållberg, A., Chávez-Galarza, J. C., Johnston, J. S., Webster, M. T., & Pinto, M. A. (2018) · Scientific Reports · doi:10.1038/s41598-018-29469-5 · Cited by 35
Delineation of crosstalk between HSP27 and MMP-2/MMP-9: A synergistic therapeutic avenue for glioblastoma management
Rajesh, Y., Banerjee, A., Pal, I., et al. (2019) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2019.04.015 · Cited by 35
Predicting changes in protein stability caused by mutation using sequence‐and structure‐based methods in a CAGI5 blind challenge
Strokach, A. V., Corbi‐Verge, C., & Kim, P. M. (2019) · Human Mutation · doi:10.1002/humu.23852 · Cited by 39
Genetic, structural, and functional characterization of POLE polymerase proofreading variants allows cancer risk prediction
Hamzaoui, N., Alarcon, F., Leulliot, N., Guimbaud, R., Buecher, B., Colas, C., Corsini, C., Nuel, G., Terris, B., Laurent‐Puig, P., et al. (2020) · Genetics in Medicine · doi:10.1038/s41436-020-0828-z · Cited by 34
Interfacial Water in the SARS Spike Protein: Investigating the Interaction with Human ACE2 Receptor and In Vitro Uptake in A549 Cells
Singh, A. V., Kayal, A., Malik, A., Maharjan, R. S., Dietrich, P., Thißen, A., Siewert, K., Curato, C., Pande, K., Prahlad, D., et al. (2022) · Langmuir · doi:10.1021/acs.langmuir.2c00671 · Cited by 38
Expanding molecular modeling and design tools to non‐natural sidechains
Gfeller, D., Michielin, O. A., & Zoete, V. (2012) · Journal of Computational Chemistry · doi:10.1002/jcc.22982 · Cited by 37
Identification and Characterization of CDH1 Germline Variants in Sporadic Gastric Cancer Patients and in Individuals at Risk of Gastric Cancer
Garziera, M., Canzonieri, V., Cannizzaro, R., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0077035 · Cited by 35
Revealing the Effects of Missense Mutations Causing Snyder-Robinson Syndrome on the Stability and Dimerization of Spermine Synthase
Peng, Y., Norris, J. W., Schwartz, C. E., & Alexov, E. G. (2016) · International Journal of Molecular Sciences · doi:10.3390/ijms17010077 · Cited by 35
Covalently immobilized catalase on functionalized graphene: effect on the activity, immobilization efficiency, and tetramer stability
Barreca, D., Neri, G., Scala, A., et al. (2018) · Biomaterials Science · doi:10.1039/c8bm00850g · Cited by 35
CDK2 and CDK4: Cell Cycle Functions Evolve Distinct, Catalysis-Competent Conformations, Offering Drug Targets
Zhang, W., Liu, Y., Jang, H., & Nussinov, R. (2024) · JACS Au · doi:10.1021/jacsau.4c00138 · Cited by 34
Structure and Dynamics of Apical Membrane Antigen 1 from Plasmodium falciparum FVO
Lim, S. S., Yang, W., Krishnarjuna, B., Sivaraman, K. K., Chandrashekaran, I. R., Kass, I., MacRaild, C. A., Devine, S. M., Debono, C. O., Anders, R. F., et al. (2014) · Biochemistry · doi:10.1021/bi5012089 · Cited by 34
Dominant Negative Mutations Affect Oligomerization of Human Pyruvate Kinase M2 Isozyme and Promote Cellular Growth and Polyploidy
Gupta, V., Ponnusamy, K., Faheem, M., Singh, N., Iqbal, M. A., & Bamezai, R. N. K. (2010) · Journal of Biological Chemistry · doi:10.1074/jbc.m109.065029 · Cited by 34
Human Proteins with Target Sites of Multiple Post-Translational Modification Types Are More Prone to Be Involved in Disease
Huang, Q., Chang, J., Cheung, M. K., Nong, W., Li, L., Lee, M.-T., & Kwan, H. S. (2014) · Journal of Proteome Research · doi:10.1021/pr401019d · Cited by 37
StructMAn: annotation of single-nucleotide polymorphisms in the structural context
Greß, A., Ramensky, V. E., Büch, J., Keller, A., & Kalinina, O. V. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw364 · Cited by 31
Differences in antigenic sites and other functional regions between genotype A and G mumps virus surface proteins
Gouma, S., Vermeire, T., Gucht, S. V., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-31630-z · Cited by 34
Expansion and diversification of the gibberellin receptor GIBBERELLIN INSENSITIVE DWARF1 (GID1) family in land plants
Gazara, R. K., Moharana, K. C., Rabelo, D. B., et al. (2018) · Plant Molecular Biology · doi:10.1007/s11103-018-0750-9 · Cited by 34
Critical effect of proline on thermostability of endoglucanase II from Penicillium verruculosum
Сергеевна, Д. А., Pramanik, S., Gusakov, A. V., et al. (2019) · Biochemical Engineering Journal · doi:10.1016/j.bej.2019.107395 · Cited by 34
Side-by-side comparison of Notch- and C83 binding to γ-secretase in a complete membrane model at physiological temperature
Dehury, B., Tang, N., Mehra, R., Blundell, T. L., & Kepp, K. P. (2020) · RSC Advances · doi:10.1039/d0ra04683c · Cited by 33
A base measure of precision for protein stability predictors: structural sensitivity
Caldararu, O. F., Blundell, T. L., & Kepp, K. P. (2021) · BMC Bioinformatics · doi:10.1186/s12859-021-04030-w · Cited by 35
De novo ATP1A3 variants cause polymicrogyria
Miyatake, S., Kato, M., Kumamoto, T., Hirose, T., Koshimizu, E., Matsui, T., Takeuchi, H., Doi, H., Hamada, K., Nakashima, M., et al. (2021) · Science Advances · doi:10.1126/sciadv.abd2368 · Cited by 34

Authors: Schymkowitz, J., Borg, J., Stricher, F., Nys, R., Rousseau, F., & Serrano, L.
Affiliations: Vrije Universiteit Brussel (BE)
University of Copenhagen (DK)
European Molecular Biology Laboratory (DE)
Corresponding author: Schymkowitz, J.
ORCID: Schymkowitz, J.
Stricher, F.
Nys, R.
Rousseau, F.
Venue: Nucleic Acids Research
Publisher: Oxford University Press (OUP)
Published: 2005-07-01
Volume: 33
Issue: Web Server
Pages: W382-W388
ISSN: 0305-1048 (ISSN-L)
1362-4962
DOI: 10.1093/nar/gki387
PMC: PMC1160148
OpenAlex: W2023490488
Semantic Scholar: 18ceb01ed1614dfc42404e0e2d838443cc0a4731
Cited by: 2,759
References: 23
Citations by year: 2026: 222 · 2025: 298 · 2024: 254 · 2023: 264 · 2022: 215 · 2021: 227 · 2020: 223 · 2019: 181 · 2018: 150 · 2017: 113 · 2016: 99 · 2015: 96 · 2014: 90 · 2013: 65 · 2012: 65
FWCI: 9.29
Type: journal article
Language: en
Open access: gold
doi.org
Licence: public-domain
Locations: Nucleic Acids Research (publishedVersion, public-domain)
Europe PMC (PubMed Central) (publishedVersion)
PubMed Central (publishedVersion)
PubMed (publishedVersion)
VUBIR (Vrije Universiteit Brussel) (submittedVersion)
Funders: European Commission
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Keywords: FoldX, empirical force fields, protein stability, free energy calculation, protein folding, protein dynamics, nucleic acids, mutation effects, proton positions, water bridges, metal binding sites, complex formation, alanine scanning
MeSH terms: Mutation, Nucleic Acid Conformation, Protein Conformation, Proteins, Software, Molecular Structure, Protein Folding, Internet, Polymorphism, Single Nucleotide, Databases, Protein

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

The FoldX web server: an online force field

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks